olgabot/psytoolkit-analysis

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Created over 2 years ago
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olgabot/psytoolkit-analysis

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Analyze psytoolkit data

prettyplotlib

Painlessly create beautiful matplotlib plots.

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

awesome-expectations

Examples of great academic lab expectations, manuals, policies for joining and being in the lab

cshl-singlecell-2017

Single Cell Analysis course at Cold Spring Harbor Laboratory 2017

Jupyter Notebook

sciencemeetproductivity.tumblr.com

backup of old blog at sciencemeetproductivity.tumblr.com

cheatsheets

Quick lookup documents for commonly used tools

abi2fastq

abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ

sj2psi

Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scores

kvector

kvector is a small utility for converting motifs to kmer vectors to compare motifs of different lengths

Jupyter Notebook

twerk

Network analysis of correlations (WGCNA-inspired)

dissertation

Computational analysis of single-cell alternative splicing: A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology

dotfiles

Collection of rc files for easy portability

codeneuro_sf2015_dataset_packaging

Notes from dataset packaging subgroup at CodeNeuro

poshsplice

PoshSplice is a collection of scripts and functions used to annotate splicing events, exons, and their functional consequences

macosko2015

Expression data for Macosko et al, "Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets," Cell (2015)

Jupyter Notebook

wasabiplot

WasabiPlot is a flexible coverage and junction read plotter that heavily borrows from MISO's SashimiPlot

gscripts

General Use Scripts and Helper functions

bonvoyage

Transform percentage-based units into a 2d space to evaluate changes in distribution with both magnitude and direction.

olgabot.github.io-source-deprecated

Source code for blog, autodeployed using Travis-CI

Jupyter Notebook

permission-letters

LaTeX template for creating co-author permission letters for UCSD dissertation submissions

Jupyter Notebook

segerstolpe_palasantza2016

Expression and metadata for Segerstolpe + Palasantza et al, "Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes" in Cell Metabolism (2016)

Jupyter Notebook

open-women

List of women in open source, open science, open access fields

pycon2014_dataviz

Computational data visualization. Presented at PyCon 2014 lightning talks.

circle-time

Circular graphic representation of time spent during the day

pydata2014biodata

Slides and ipython notebooks accompanying talk given at PyData NYC 2014

pyhomer

Utility functions to work with output from the HOMER motif finding program

rnaseek

Scripts and modules for parsing and aggregating output files from RNA-sequencing data

nextflow-each-metadata-error

Repo to test nextflow `each` directive with metadata